Labor shadow treasurer Chris Bowen wrote to Mr Gaetjens on Friday to demand an explanation for the government's use of "Treasury costings" to attack the Labor policies.

Mr Gaetjens replied with confirmation the department prepared the cost estimates, but he made it clear these were based on instructions from the government.

"We were not asked to cost another party's policies and would not do so if the request was made specifically to 'cost Party X's policy'," Mr Gaejtens wrote to Mr Bowen.

"In providing specific costings to the government at its request, Treasury advised they were all costed on a standalone basis but with interactions between the individual proposals not taken into account. For this reason we did not provide a total."

The government has insisted the costings are accurate because Treasury has costed the alternative policies. The $387 billion figure is very close to the total for Labor's own cost estimates for its policies. Labor has not disputed specific numbers in the new costings, released on Friday.

Treasury has previously costed opposition policies by taking an announced policy and modelling it in the same way it would a government policy.

A Treasury spokesman told The Sydney Morning Herald and The Age the request for the costings came from the government.

"Treasury received requests from the Treasurer's office outlining a number of policies to be costed. The requests made no reference to the Opposition," a spokesperson said.

"The relevant policy officers costed these proposals and provided this analysis to the Treasurer's office prior to the commencement of the caretaker period."

Mr Gaetjens stood by the Treasury's work and noted the department would always do the work asked of it by the government of the day whenever there is a "lawful request" of the officials.

The Treasury Secretary noted a previous dispute over costings in 2012 when the department said it served the Australian people through the government of the day.

Prime Minister Scott Morrison said on Friday that the "Treasury costings" revealed $387 billion in higher taxes under Labor, while Treasurer Josh Frydenberg said the estimate showed Labor would impose "$387 billion in new taxes" over a decade.

Mr Bowen spoke to Mr Gaetjens on Friday morning and wrote to him soon afterwards to warn of his "deep concern" at the use of Treasury for the Coalition's political advantage.

"It is critical that Treasury is seen as impartial and credible and not politicised by the government of the day," Mr Bowen said in the letter.

"As you are aware, it has been a long-standing position by the Treasury that it does not cost opposition policies.

"This is a matter that has come up multiple times at Senate estimates over the last year and in correspondence with former Treasury Secretary, John Fraser."

Labor has previously warned against the appointment of Mr Gaetjens to the position of Treasury Secretary on the grounds he was previously chief of staff to Mr Morrison as treasurer and chief of staff to Peter Costello as treasurer.

Mr Bowen said that Mr Morrison had been caught "lying" about the Labor policies.

The $387 billion estimate is the Coalition's total based on Treasury estimates of policies including changes to negative gearing, dividend imputation and family trusts.

The estimates are close to those prepared by Labor itself based on work from the Parliamentary Budget Office.

The Coalition said it received the cost estimates from Treasury after the budget on April 2.

The $387 billion estimate shows the scale of the taxes under a Labor government over 10 years according to its stated policies compared to the budget plan set out by the Coalition.

While the government has claimed these are "new taxes" on Australians, the biggest single component is $230 billion in revenue from Labor's rejection of the Coalition's personal income tax cuts. This means Labor is keeping the status quo rather than applying new taxes.

Another $157 billion in higher revenue comes from Labor policy initiatives from negative gearing, dividend changes, family trusts and superannuation.

SMH/The Age